Heatmap and rna-seq

Question

[qudrat.nii]

Hello everyone!

I have a list of pathways from GSEA analysis (RNA-Seq data) and I want to plot a heatmap of genes associated with pathways, showing distinctly each pathway in the heatmap. Can somebody help me with this

[Basti]

This forum is not dedicated to this type of request, there are many online tutorials for creating heatmaps accessible with simple internet searches. If you have a more specific question related to the code you are using, then we will be able to help

[Istvan Albert]

This forum is dedicated to asking their question on bioinformatics. As long as the topic is bioinformatics, all questions are welcome, and it would be more helpful if you pointed the OP to specific tools you know work well.

Some tools work much better than others, and people that have experience with the process that can provide the best guidance, not a Google search - that in the end will go to forums like this ...

Answer 1

[pinheirofabiano]

install.packages("pheatmap")

library(pheatmap)

setwd("/Users/data_analysis/results")

data <- read.table(file = "log2cpm.tsv", header = T, sep = "\t")

pheatmap(mat = data)

Answer 2

[dsull]

Check out clustergrammer from Avi Ma'ayan's lab.

[GenoMax]

Please include a link when you are recommending a tool. There can be programs with similar names.

[dsull]

https://maayanlab.cloud/clustergrammer/

It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pathway x gene matrix or a sample x gene matrix.

Answer 3

[Kevin Blighe]

Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap.

You have not indicated that you require assistance with coding; so, I will end my answer right here.

Kevin